Tapping the wealth of microbial data in high-throughput metabolic model reconstruction

Genome-scale metabolic models are valuable tools in the metabolic engineering process, based on the ability of these models to integrate diverse sources of data to produce global predictions of organism behavior. At the most basic level, these models require only a genome sequence to construct, and once built, they may be used to predict essential genes, culture conditions, pathway utilization, and the modifications required to enhance a desired organism behavior. In this chapter, we address two key challenges associated with the reconstruction of metabolic models: (a) leveraging existing knowledge of microbiology, biochemistry, and available omics data to produce the best possible model; and (b) applying available tools and data to automate the reconstruction process. We consider these challenges as we progress through the model reconstruction process, beginning with genome assembly, and culminating in the integration of constraints to capture the impact of transcriptional regulation. We divide the reconstruction process into ten distinct steps: (1) genome assembly from sequenced reads; (2) automated structural and functional annotation; (3) phylogenetic tree-based curation of genome annotations; (4) assembly and standardization of biochemistry database; (5) genome-scale metabolic reconstruction; (6) generation of core metabolic model; (7) generation of biomass composition reaction; (8) completion of draft metabolic model; (9) curation of metabolic model; and (10) integration of regulatory constraints. Each of these ten steps is documented in detail.

FISHji: new ImageJ macros for the quantification of fluorescence in epifluorescence images

Fluorescence in situ hybridization (FISH) is based on the use of fluorescent staining dyes, however, the signal intensity of the images obtained by microscopy is seldom quantified with accuracy by the researcher. The development of innovative digital image processing programs and tools has been trying to overcome this problem, however, the determination of fluorescent intensity in microscopy images still has issues due to the lack of precision in the results and the complexity of existing software. This work presents FISHji, a set of new ImageJ methods for automated quantification of fluorescence in images obtained by epifluorescence microscopy. To validate the methods, results obtained by FISHji were compared with results obtained by flow cytometry. The mean correlation between FISHji and flow cytometry was high and significant, showing that the imaging methods are able to accurately assess the signal intensity of fluorescence images. FISHji are available for non-commercial use at http://paginas.fe.up.pt/nazevedo/.

Ingeniería de glicanos: diseño de inmunógenos y ligandos de lectinas. Glycan engineering: design of immunogens and ligand of lectins.

La ingeniería de glicanos es un área de investigación emergente, la que posee múltiples aplicaciones en medicina. Mediante esta herramienta se intentará reducir la flexibilidad de las uniones glicosídicas de antígenos tumorales, como la del antígeno T (Galbeta3GalNAcalfa-Ser/Thr). Aquí se realizarán las menores alteraciones posibles en la topología de glicanos que generen la mejor respuesta inmune hacia el antígeno de interés. Por otra parte, se buscará ligandos de alta afinidad que interaccionen con lectinas involucradas en diseminación de metástasis. Mediante ensayos teóricos de Docking se tratará de hallar modificaciones topológicas de glicanos que potencialmente tengan propiedades anti-adhesivas para células tumorales. Este proyecto constará de tres etapas: una teórica, utilizando programas de cálculos para ensayos de Docking y mínimos energéticos de glicanos. Otra de síntesis, generando los glicoconjugados sugeridos en la etapa anterior. En la última, se verificará si estos glicanos rediseñados adquirieron las propiedades biológicas deseadas. Así se determinará si generan una respuesta inmune que reconozca antígenos y células tumorales. También, se analizarán las propiedades anti-adhesivas de los glicanos utilizando diferentes modelos experimentales. Finalmente, se determinará si los inmunógenos producidos y/o glicoconjugados rediseñados poseen efecto en el desarrollo tumoral y sobrevida animal.

Application of multivariate statistical process control to fuel cell manufacturing

Univariate statistical control charts, such as the Shewhart chart, do not satisfy the requirements for process monitoring on a high volume automated fuel cell manufacturing line. This is because of the number of variables that require monitoring. The risk of elevated false alarms, due to the nature of the process being high volume, can present problems if univariate methods are used. Multivariate statistical methods are discussed as an alternative for process monitoring and control. The research presented is conducted on a manufacturing line which evaluates the performance of a fuel cell. It has three stages of production assembly that contribute to the final end product performance. The product performance is assessed by power and energy measurements, taken at various time points throughout the discharge testing of the fuel cell. The literature review performed on these multivariate techniques are evaluated using individual and batch observations. Modern techniques using multivariate control charts on Hotellings T2 are compared to other multivariate methods, such as Principal Components Analysis (PCA). The latter, PCA, was identified as the most suitable method. Control charts such as, scores, T2 and DModX charts, are constructed from the PCA model. Diagnostic procedures, using Contribution plots, for out of control points that are detected using these control charts, are also discussed. These plots enable the investigator to perform root cause analysis. Multivariate batch techniques are compared to individual observations typically seen on continuous processes. Recommendations, for the introduction of multivariate techniques that would be appropriate for most high volume processes, are also covered.

Teaching Basic Life Support to Students of Public and Private High Schools

Background:Despite being recommended as a compulsory part of the school curriculum, the teaching of basic life support (BLS) has yet to be implemented in high schools in most countries.Objectives:To compare prior knowledge and degree of immediate and delayed learning between students of one public and one private high school after these students received BLS training.Methods:Thirty students from each school initially answered a questionnaire on cardiopulmonary resuscitation (CPR) and use of the automated external defibrillator (AED). They then received theoretical-practical BLS training, after which they were given two theory assessments: one immediately after the course and the other six months later.Results:The overall success rates in the prior, immediate, and delayed assessments were significantly different between groups, with better performance shown overall by private school students than by public school students: 42% ± 14% vs. 30.2% ± 12.2%, p = 0.001; 86% ± 7.8% vs. 62.4% ± 19.6%, p < 0.001; and 65% ± 12.4% vs. 45.6% ± 16%, p < 0.001, respectively. The total odds ratio of the questions showed that the private school students performed the best on all three assessments, respectively: 1.66 (CI95% 1.26-2.18), p < 0.001; 3.56 (CI95% 2.57-4.93), p < 0.001; and 2.21 (CI95% 1.69-2.89), p < 0.001.Conclusions:Before training, most students had insufficient knowledge about CPR and AED; after BLS training a significant immediate and delayed improvement in learning was observed in students, especially in private school students.

Relationship between Neutrophil-To-Lymphocyte Ratio and Electrocardiographic Ischemia Grade in STEMI

Background: Neutrophil-to-lymphocyte ratio (NLR) has been found to be a good predictor of future adverse cardiovascular outcomes in patients with ST-segment elevation myocardial infarction (STEMI). Changes in the QRS terminal portion have also been associated with adverse outcomes following STEMI. Objective: To investigate the relationship between ECG ischemia grade and NLR in patients presenting with STEMI, in order to determine additional conventional risk factors for early risk stratification. Methods: Patients with STEMI were investigated. The grade of ischemia was analyzed from the ECG performed on admission. White blood cells and subtypes were measured as part of the automated complete blood count (CBC) analysis. Patients were classified into two groups according to the ischemia grade presented on the admission ECG, as grade 2 ischemia (G2I) and grade 3 ischemia (G3I). Results: Patients with G3I had significantly lower mean left ventricular ejection fraction than those in G2I (44.58 ± 7.23 vs. 48.44 ± 7.61, p = 0.001). As expected, in-hospital mortality rate increased proportionally with the increase in ischemia grade (p = 0.036). There were significant differences in percentage of lymphocytes (p = 0.010) and percentage of neutrophils (p = 0.004), and therefore, NLR was significantly different between G2I and G3I patients (p < 0.001). Multivariate logistic regression analysis revealed that only NLR was the independent variable with a significant effect on ECG ischemia grade (odds ratio = 1.254, 95% confidence interval 1.120–1.403, p < 0.001). Conclusion: We found an association between G3I and elevated NLR in patients with STEMI. We believe that such an association might provide an additional prognostic value for risk stratification in patients with STEMI when combined with standardized risk scores.

Automatisierte Hardware-Software Partitionierung am Beispiel eines eingebetteten, echtzeitfähigen Stereobildanalysesystems in Kraftfahrzeugen

Hardware-Software Co-Design, Simulated Annealing, Real-Time Image Processing, Automated Hardware-Software Partitioning

Can climate shape flight activity patterns of Plebeia remota Hymenoptera, Apidae)?

Flight activity of foragers of four colonies of Plebeia remota (Holmberg, 1903) was registered from December 1998 to December 1999, using an automated system (photocells and PLC system). The colonies originated from two different regions: Cunha, state of São Paulo, and Prudentópolis, state of Paraná, Brazil. Flight activity was influenced by different climatic factors in each season. In the summer, the intensity of the correlations between flight activity and climatic factors was smaller than in the other seasons. During the autumn and winter, solar radiation was the factor that most influenced flight activity, while in the spring, this activity was influenced mainly by temperature. Except in the summer, the various climatic factors similarly influenced flight activity of all of the colonies. Flight activity was not affected by geographic origin of the colonies. Information concerning seasonal differences in flight activity of P. remota will be useful for prediction of geographic distribution scenarios under climatic changes.

Estudio para la extracción automatizada de contextos de significancia en JPEG2000

Se ha desarrollado un trabajo de investigación para arrojar un haz de luz en ciertas regiones de interés en la codificación del estándar JPEG2000. La finalidad de esta investigación, es estudiar la posibilidad de realizar una extracción automatizada de contextos durante el proceso de codificación, de modo que se ajusten a la imagen procesada y observar qué ventajas nos aporta esto frente a los contextos establecidos por el estándar JPEG2000.

Una primera aproximació a la selecció d'un sistema automatitzat de biblioteques

Res no pot garantir que un procés de selecció d'un sistema automatitzat arribi a tenir èxit, però l'observació d'un conjunt de principis de sentit comú pot ajudar a assegurar l'èxit del resultat. El procés ha de centrar-se en el llarg termini i ha de tenir present el context institucional en el qual el sistema s'establirà. Els sistemes estan cada vegada més orientats als usuaris, i per tant el compromís dels usuaris en el procés de selecció és més i més important. Els components del procés de selecció poden ser previstos i combinats de moltes maneres diferents. El procediment usat per les Purdue University Libraries serveix per a il·lustrar una via en la realització pràctica d'un procés.

Modeling sequencing errors by combining Hidden Markov models.

Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.

Automatización de la gestión del ciclo de vida de entornos Linux y Solaris

Los requisitos del Negocio que requieren un gran crecimiento generan mayor complejidad en los Centros de Cómputo.Son los administradores quienes necesitan gestionar el creciente volumen de datos, aplicaciones, y usuarios, así como la rápida proliferación de los servidores y los diferentes sistemas operativos. En este proyecto se pretende reducir la complejidad en la gestión de los Centros de Cómputo, combinando la automatización de la gestión del ciclo de vida y todas las medidas de contingencia necesarias para mantener la integridad de los mismos.

Long-term fluctuation of relative afferent pupillary defect in subjects with normal visual function.

PURPOSE: To determine whether the relative afferent pupillary defect (RAPD) remains constant over time in normal subjects. METHODS: Seventeen normal subjects were tested with infrared pupillography and automated perimetry in four sessions over 3 years. The changes in RAPD and visual field asymmetry between testing sessions were compared. RESULTS: The range of RAPD was 0.0 to 0.3 log unit, and the difference in the mean deviation between the eyes on automated static perimetry was 0 to 3 dB. Eight subjects repeatedly had an RAPD in the same eye. There was no correlation between the RAPD and the visual field asymmetry at the same visit. Changes in the magnitude of the RAPD between any two sessions were typically small (median, 0.08 log unit; 25th percentile, 0.04 log unit; 75th percentile, 0.15 log unit). CONCLUSIONS: Some normal subjects may show a persistent but small RAPD in the absence of detectable pathologic disease. Therefore, an isolated RAPD in the range of 0.3 log unit that is not associated with any other significant historical or clinical finding should probably be considered benign.

Theoretical study on receptor-G protein recognition: new insights into the mechanisms of the alpha1b-adrenergic recptor activation

This work compares the structural/dynamics features of the wild-type alb-adrenergic receptor (AR) with those of the D142A active mutant and the agonist-bound state. The two active receptor forms were compared in their isolated states as well as in their ability to form homodimers and to recognize the G alpha q beta 1 gamma 2 heterotrimer. The analysis of the isolated structures revealed that, although the mutation- and agonist-induced active states of the alpha 1b-AR are different, they, however, share several structural peculiarities including (a) the release of some constraining interactions found in the wild-type receptor and (b) the opening of a cytosolic crevice formed by the second and third intracellular loops and the cytosolic extensions of helices 5 and 6. Accordingly, also their tendency to form homodimers shows commonalties and differences. In fact, in both the active receptor forms, helix 6 plays a crucial role in mediating homodimerization. However, the homodimeric models result from different interhelical assemblies. On the same line of evidence, in both of the active receptor forms, the cytosolic opened crevice recognizes similar domains on the G protein. However, the docking solutions are differently populated and the receptor-G protein preorientation models suggest that the final complexes should be characterized by different interaction patterns.

Testing low-altitude infrared digital photography from a mini-UAV to retrieve information for biological conservation

Satellite remote sensing imagery is used for forestry, conservation and environmental applications, but insufficient spatial resolution, and, in particular, unavailability of images at the precise timing required for a given application, often prevent achieving a fully operational stage. Airborne remote sensing has the advantage of custom-tuned sensors, resolution and timing, but its price prevents using it as a routine technique for the mentioned fields. Some Unmanned Aerial Vehicles might provide a “third way” solution as low-cost techniques for acquiring remotely sensed information, under close control of the end-user, albeit at the expense of lower quality instrumentation and instability. This report evaluates a light remote sensing system based on a remotely-controlled mini-UAV (ATMOS-3) equipped with a color infra-red camera (VEGCAM-1) designed and operated by CATUAV. We conducted a testing mission over a Mediterranean landscape dominated by an evergreen woodland of Aleppo pine (Pinus halepensis) and (Holm) oak (Quercus ilex) in the Montseny National Park (Catalonia, NE Spain). We took advantage of state-of-the-art ortho-rectified digital aerial imagery (acquired by the Institut Cartogràfic de Catalunya over the area during the previous year) and used it as quality reference. In particular, we paid attention to: 1) Operationality of flight and image acquisition according to a previously defined plan; 2) Radiometric and geometric quality of the images; and 3) Operational use of the images in the context of applications. We conclude that the system has achieved an operational stage regarding flight activities, although with meteorological limits set by wind speed and turbulence. Appropriate landing areas can be sometimes limiting also, but the system is able to land on small and relatively rough terrains such as patches of grassland or short matorral, and we have operated the UAV as far as 7 km from the control unit. Radiometric quality is sufficient for interactive analysis, but probably insufficient for automated processing. A forthcoming camera is supposed to greatly improve radiometric quality and consistency. Conventional GPS positioning through time synchronization provides coarse orientation of the images, with no roll information.